Activity for Open Babel
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Anonymous created ticket #105
eman1
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Anonymous created ticket #104
Defined partial charges in OBForceField
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Anonymous created ticket #103
Segmentation fault (core dumped) error while generating 3D coordinates from .sdf files
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Anonymous posted a comment on ticket #40
mol2kcf source ftp://ftp.genome.jp/pub/tools/simcomp/kcfco-1.1.2.tar.gz
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Noel O'Boyle modified a comment on ticket #102
Hi there. I thought it was no longer possible to post tickets here. It seems I was wrong. There was a notice at the top of the submission page with the following info: The File Format Support tracker for Open Babel here at sourceforge.net is in read-only mode. It presents the state of Open Babel file format support tickets in March 2017. Tickets are now managed at https://github.com/openbabel/openbabel/issues Go there to submit new tickets, comment on existing tickets, or follow ongoing efforts to...
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Hi there. I thought it was no longer to post tickets here. It seems I was wrong. There was a notice at the top of the submission page with the following info: The File Format Support tracker for Open Babel here at sourceforge.net is in read-only mode. It presents the state of Open Babel file format support tickets in March 2017. Tickets are now managed at https://github.com/openbabel/openbabel/issues Go there to submit new tickets, comment on existing tickets, or follow ongoing efforts to service...
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Anonymous created ticket #102
Enumerate atoms when converting sdf to mol2
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This bug is closed. See https://github.com/openbabel/openbabel/issues/1140 and the notice about this SourceForge bug tracker at the top of https://sourceforge.net/p/openbabel/bugs/. If you have found a new bug, please file it on Github as described in that notice.
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Termo posted a comment on ticket #760
And more weird stuff when looking at bond orders for the input inchi molecule: [b.GetBondOrder() for b in ob.OBMolBondIter(mol)] Out[40]: [2, 1, 1, 2, 2, 2, 1, 1, 1, 1] and the output of a small function I have made to give a bond dict: getbsum('InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-4H', term='inchi') Out[43]: [defaultdict(int, {'[C]-1-[C]': 2, '[C]-1-[H]': 4, '[C]-2-[C]': 4}), #C 6 #H 4 dtype: int64] So 4 double bonds (should be 2) and no triple bonds (should be 1) ??
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How can this bug still stick around? I just ran into it with Benzyne 'c1ccccc#1', which I suddenly found had wrong atomic count in my database... obabel -ismi -:'c1ccccc#1' -oreport -h FILENAME: FORMULA: C6H6 MASS: 78.1118 obabel -iinchi -:'InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-4H' -oreport -h FILENAME: FORMULA: C6H4 MASS: 76.0960 Open Babel 2.4.1 -- Jan 19 2017
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How can this bug still stick around? I just ran into it with Benzyne 'c1ccccc#1', which I suddenly found had wrong atomic count in my database... obabel -ismi -:'c1ccccc#1' -oreport -h FILENAME: FORMULA: C6H6 MASS: 78.1118 obabel -iinchi -:'InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-4H' -oreport -h FILENAME: FORMULA: C6H4 MASS: 76.0960
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obminimize gives warnings
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Pent posted a comment on ticket #994
Ah, it works in a new command prompt without warnings! Please close.
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The environment variable BABEL_DATADIR is either not set, or pointing to a location...
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obminimize gives warnings
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InChI to SVG stereochemical layer silent error
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Works for me with OB 2.4.1. I recall that I fixed an InChI bug at some point.
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Duncan Hampshire created ticket #993
InChI to SVG stereochemical layer silent error
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Thomas Griffiths created ticket #992
Charges output wrong when converting CDX to GJF/COM/GAU/GJC
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Andrew Dalke created ticket #991
Universal SMILES with "*" causes executable to abort
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Michael Kausch created ticket #990
Obconformer does not return lowest energy conformer
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Derek Harmon modified a comment on ticket #909
This trivial patch (against OpenBabel 2.3.2 source) will prevent the segmentation...
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This trivial patch (against OpenBabel 2.3.2 source) will prevent the segmentation...
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This trivial patch (against OpenBabel 2.3.2 source) will prevent the segmentation...
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I can reproduce this behavior on CentOS 6.7 using OpenBabel 2.3.2 and a build of...
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I e-mailed the original poster of https://sourceforge.net/p/openbabel/mailman/message/34502202/...
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Good point, GetX(), etc. is probably the best way. GetVector() is working, but if...
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Fabio Lolicato posted a comment on ticket #988
It is making sense. Thanks for prompt reply. Just for completeness , also OBAtom.GetVector()...
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This is correct, but as the coordinates are accessible via OBAtom.GetVector(), I...
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Jernej Zidar created ticket #989
Lost of connectivity data during minimization, conversion of MOL2 files
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OBMol.GetCoordinates() do not work.
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OBForceField functions ignore convergence criteria
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Shuo Zhou created ticket #986
mol2 to pdbqt atom type conversion bug
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Luis M. Sánchez created ticket #985
pdf multichain exports to fasta monochain
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models extracted from pdb files must be renumbered
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cml embedded inside svg lacks stereo information
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Still present in Open Babel 2.4.1 on Windows 7.
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Error converting ORCA output files
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Confirmed with latest version 2.4.1 (64bit) on Win10pro 64bit used from the command-line....
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Matthias Budzynski created ticket #981
Error converting xyz containing heteroaromatics to mol (version 2.4.1)
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Roman Kudrin created ticket #980
Segfault while converting mopout to pdb
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MMatlock posted a comment on ticket #979
On futher contemplation, it appears that openbabel at first thinks the adjacent ring...
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OpenBabel incorrectly removes aromaticity from triazole compound(s)
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wannursyakilla created ticket #978
Error in Installing Open Babel
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annyoinglogin posted a comment on ticket #977
Expected output should just be the inchi
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[CRITICAL ERROR] If you .write as an inchi, a core dump happens.
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Error in converting cdx files with functional group aliases
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Open Babel 2.4.0 Released
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Open Babel released /openbabel/2.4.0/OpenBabel-2.4.0.exe
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Anonymous created ticket #101
c3xml
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Ronald Cohen created ticket #974
Bug in CIF input and monoclinic space groups
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Terrance Vincente created ticket #973
latest Java Binding crashes JVM in MAC OSX 10.9.5 with Java 7&8 JVMs
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Sebastian ECHEVERRI RESTREPO posted a comment on ticket #972
The structure of the file is correct. The problem is the connectivity of the atoms....
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Geoff Hutchison posted a comment on ticket #972
Can you be a bit more specific about "not properly generated?" I don't use LAMMPS...
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Bug generation of bonds lmpdat
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Felix Plasser created ticket #971
Bug in conversion of Molden file
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Stefano Forli created ticket #970
OBBond.IsEster(): mis-identification of carboxylic acids
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Andre created ticket #174
Addition of Extra Point of Charge to halides
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Not a bug. That's the docs for the dev version, which cannot be downloaded for windows...
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Zoli Fekete created ticket #969
"confab is not a recognized plugin type." in Open Babel 2.3.2
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Pradeep Verma created ticket #968
OBDotNet : The type initializer for 'OpenBabel.openbabel_csharpPINVOKE' threw an exception. Unable to load DLL 'openbabel_csharp'
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Here is the file.
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moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe
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Alfredo Correa created ticket #966
Bad symbols in elements database!
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Anonymous created ticket #100
probelm with converting .res file
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Christoph Helma posted a comment on ticket #957
I can confirm that the latest master branch (commit 7be9ee2fb614bfc5a2c0ffa97a14f94815ea5382)...
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Matej Repic posted a comment on ticket #965
System info: Open Babel 2.3.2 -- Dec 19 2014 -- 19:23:22 from Macports Darwin bond...
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Incorrect hydrogen handling while converting pdb to svg
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I am running on Arch Linux with todays master branch from github and still get segfaults...
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Opem Babel misses hydrogen from InChI or from MDL MOL file
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Patrick Avery posted a comment on ticket #963
Oops. I guess this should have been labeled 2.3.x
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Windows compilation - Missing dll's?
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Henrique Musseli Cezar created ticket #962
Python SWIG - Error when calling OBRotorList::Init
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Memory Leak in Python Swig inteface (OBRotor object)
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Seems to be working fine for me now with the development version: echo "InChI=1/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1/f/h8H,6H2"...
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Interpretation of InChI's stereochemical layer in obabel 2.3.3
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Segmentation fault for converting InChi to MDL
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This appears to be working now with the current development code (I confirm that...
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Null pointer dereference in OpenBabel::OBSmilesParser::ParseSmiles
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This appears to be fixed in the current development code: *** Open Babel Warning...
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Witek Mozga created ticket #173
Inverted search with fast search index
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zetadin modified a comment on ticket #960
I managed to fix the memory issues in my local working copy of the trunk. OBMol::Clear()...
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I managed to fix the memory issues in my local working copy of the trunk. OBMol.Clear()...
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Incorrect memory managment of conformer coordinates when reading xtc files
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